Aims Poor oral hygiene can provoke transient bacteremia and systemic inflammation, a mediator of atrial fibrillation and heart failure. This study aims to investigate association of oral hygiene indicators with atrial fibrillation and heart failure risk in Korea. Methods We included 161,286 subjects from the National Health Insurance System-Health Screening Cohort who had no missing data for demographics, past history, or laboratory findings. They had no history of atrial fibrillation, heart failure, or cardiac valvular diseases. For oral hygiene indicators, presence of periodontal disease, number of tooth brushings, any reasons of dental visit, professional dental cleaning, and number of missing teeth were investigated. Results During median follow-up of 10.5 years, 4911 (3.0%) cases of atrial fibrillation and 7971 (4.9%) cases of heart failure occurred. In multivariate analysis after adjusting age, sex, socioeconomic status, regular exercise, alcohol consumption, body mass index, hypertension, diabetes, dyslipidemia, current smoking, renal disease, history of cancer, systolic blood pressure, blood and urine laboratory findings, frequent tooth brushing (≥3 times/day) was significantly associated with attenuated risk of atrial fibrillation (hazard ratio: 0.90, 95% confidence interval (0.83–0.98)) and heart failure (0.88, (0.82–0.94)). Professional dental cleaning was negatively (0.93, (0.88–0.99)), while number of missing teeth ≥22 was positively (1.32, (1.11–1.56)) associated with risk of heart failure. Conclusion Improved oral hygiene care was associated with decreased risk of atrial fibrillation and heart failure. Healthier oral hygiene by frequent tooth brushing and professional dental cleaning may reduce risk of atrial fibrillation and heart failure.